When we left off at the end of Part I of my summary of The Wrath of Khan, things were in a bad way. The Enterprise has been badly damaged, they can't reach anybody at the science station on Regula I, and a group of genetically enhanced superpeople led by Khan, who blames Kirk for all his problems, is on the loose and after the Genesis project. The only bright spot in all of this is that Kirk managed to bring down the shields on the Reliant- Khan's ship- and inflict enough damage that it's had to temporarily withdraw from the battle. Leaving Spock to head up repairs on the Enterprise, Kirk leads an away team down to the station to find out what's happened. This includes Lt. Saavik and Dr McCoy.
On Regula I, they find the bodies of the research team hanging... they've all been tortured and killed. They also find Chekov and Terrell, who tell them that Khan tortured the scientists, demanding to know the location of the Genesis device. When they wouldn't tell him, Khan went crazy and slit their throats. They also tell them that the crew of the Reliant was left behind on Ceti Alpha V. Shortly after this, they find that the station's transporter system has recently been used, and the coordinates lead to a nearby asteroid. Kirk figures that, if they had reached test stage for the Genesis device, those tests might well be taking place on the asteroid. Kirk contacts the Enterprise, telling Spock what's going on and asking for a damage report. Spock says that it will be two days before they will have the transporters online and be able to beam them up. In the meantime, Kirk and his team beam over to the asteroid, materializing in a subterranean chamber.
They are immediately attacked by David Marcus and another scientist, who are trying to protect the Genesis device. Kirk makes short work of David, who is a researcher, not a fighter, but stops punching him when he hears Carol say David's name. David accuses Kirk of trying to take Genesis, but Carol tells her son that of course he's not. She tries to calm everyone down, but then Terrell and Chekov, who are still being mind-controlled by Khan, pull out phasers. They kill the other scientist, and Khan, in contact with the two men, tells them to shoot and kill Kirk. Terrell fights to regain control, and succeeds in turning his gun on himself instead of Kirk.
Chekov also struggles to regain control, then suddenly screams, grabbing hold of his head, and collapses. To everyone's horror, the creature, much bigger than it had been before, slithers out of his ear, and is phasered by Kirk. Chekov is still alive, but in bad shape. And then the Genesis device is beamed away by Khan, who had gotten the coordinates from Terrell and Chekov. An enraged Kirk grabs Terrell's fallen communicator and calls out Khan. Khan is shocked that KIrk is still alive, having assumed from the sound of phaser fire that his order had been carried out.
Kirk taunts him, saying that he's a poor marksman who keeps missing his target. He tell Khan that if he wants to kill him, he'll have to come down to the asteroid to do it. But a gloating Khan says he's done far worse than kill Kirk: he's hurt him, and intends to go on hurting him by leaving him "buried alive" on the asteroid while Khan and his people destroy the Enterprise and go on their way with a weaponized Genesis device. And then we have the scene which has launched a thousand memes: Kirk, in a rage, screaming Khan's name into the communicator.
David is still behaving in a hostile manner, and to get him out from under foot for a few minutes, Kirk asks him about getting some food. David grudgingly takes Saavik and McCoy into the Genesis cavern, giving Kirk and Carol a few minutes to speak privately. And now we find out that David is Kirk's son, but that he has stayed out of his life, at Carol's request. She hasn't even told David that Kirk is his father. Carol asks Kirk what he's feeling... he tells her that there's a man whom he hasn't seen in fifteen years trying to kill him, and now he's met his son, who would be happy to help with the job. He tells her that he feels old. She says that she'll show him something which will make him feel young, and leads him into the Genesis cave, which is a mini paradise.
While they wait around in the cave, Saavik asks Kirk to tell her how he succeeded in the Kobayachi Maru. Kirk says that he reprogrammed the computer, changing the variables of the simulation. David says snarkily that Kirk cheated, but Kirk tells them that he got a commendation for "original thinking". Saavik ponders this for a minute, then points out that Kirk never had to face the no-win scenario. Kirk tells her that he doesn't believe in the no-win situation then, noting the time, contacts Spock and asks if he's ready to beam them up. Everyone else is astonished, because it's only been a couple of hours, not the days which Spock had said were necessary to get the transporters back online. Kirk and Spock, however, had been going on the assumption that Khan was monitoring their transmissions, and so spoke in code, using "days" to represent "hours". As they prepare to beam up, Kirk looks over at Saavik and tells her that he doesn't like to lose.
When they get back to the Enterprise, they find that, while the transporters are working again, not much else is- not even the lifts, so they must scurry up and down Jeffries tubes to get to the bridge. They have limited power and speed, sensors are offline, and they still can't get the shields up. And the Reliant is once again closing on their position. Spock and Kirk confer, and decide to head the Enterprise into the nearby Mutara Nubula.This confuses Saavik, as it's well known that the ionized gasses of the nebula disrupt sensors and shields. Spock explains to her, "Sauce for the goose..."; the Enterprise's shields and sensors are already crippled. In the nebula however, the Reliant will lose theirs as well, evening the odds. Of course, this will only work if the Reliant follows them into the nebula, which it is understandably reluctant to do.
, As the Reliant hesitates at the edge of the nebula, Khan demands to know why they're slowing down. Joachim explains that if they enter, they'll be flying blind, without sensors or shields. Despite his obsession, Khan is inclined to listen to this warning, and they come to a stop. Knowing that he has to get the Reliant into the nebula, Kirk contacts Khan, who is enraged to find out that Kirk has somehow escaped the asteroid. Kirk goads him even further, telling him: "... I'm laughing at the 'superior intellect.'" That does it. Beside himself with rage, Khan orders the Reliant into the Mutara Nebula. Joachim protests, saying that they have Genesis, and can go anywhere and do anything they want. But Khan is fixated on killing Kirk, and so the Reliant enters the nebula, immediately losing its shields and sensors. Having to use only intermittent visual, the two ships warily search for each other in the murky nebula. The Enterprise catches a brief glimpse of the Reliant, and Kirk orders Sulu to fire phasers,"best guess," since the targeting computer is also not functioning. He guesses pretty well: some of his shots hit the Reliant, which sustains some damage. As the ships blindly search for each other, the static suddenly clears for a moment, revealing that the two ships are about to collide. As they bank sharply away from each other, both fire at point blank range. Both ships sustain heavy damage, but the Reliant gets the worst of it, also suffering heavy casualties. Among the dead is Joachim, who doesn't even get a chance to say "I told you so." As he dies, Khan vows to avenge him.
Kirk knows that he must gain some sort of tactical advantage over Khan, and Spock points out that, while Khan is brilliant, he is also inexperienced, and his tactics reflect two-dimensional thinking. Kirk mulls this over for a moment, then orders the Enterprise to drop down, well below the level of the Reliant. While this is happening, a recovered if somewhat shaky Chekov arrives on the bridge, asking to be allowed back on duty. Kirk assigns him to the weapons station.
The Reliant passes over top of them, and Kirk orders the Enterprise to rise, catching the Reliant off guard and pummeling it with phaser fire. The Reliant is dead in space, and almost all of Khan's men are dead as well. Khan is still alive, although he's sustained what looks like third degree burns to his face and arms... or maybe fourth or fifth degree: he looks pretty bad.
Naturally, he doesn't even now give up his quest for vengeance and arms the Genesis device, planning to take out the entire nebula with it. The Enterprise picks up a sudden power surge coming from the Reliant, but don't know what it's from until David looks at the computer screen and recognizes the Genesis wave. Kirk says that they'll beam over and shut it down, but David tells him that once it's been activated, Genesis can't be shut down. It's going to detonate in about four minutes and take everything in the blast zone with it. This normally wouldn't be a problem, except that the Enterprise's warp drive is still offline, leaving them with only impulse power which won't get them out of there fast enough.
Kirk orders them to head out of the nebula as quickly as they can on impulse power, then contacts the engine room, telling Scotty that they need the warp drive back online within four minutes or they're all dead. Unfortunately, he can't get a response; the engine room was one of the areas hit in the last attack, and there are quite a few casualties. Dr. McCoy is on site, treating them, but Scotty is still unconscious. Listening to Kirk trying to raise a response from engineering, Spock quietly gets up and leaves the bridge unnoticed, headed for the engine room.
The problem with fixing the warp drive is that the area it's contained in has been flooded with radiation which will kill anyone who enters it. When Spock starts to do just that, McCoy refuses to let him, but Spock pulls the old "what's that over there?" routine (or in this case, the "how's Mr. Scott?" routine) and then nerve pinches McCoy. Right after Spock enters the containment area, Scotty regains consciousness and frantically starts pounding on the door, telling Spock to get out of there. Spock ignores him; though the radiation is killing him, due to his superior Vulcan strength he is able to get the warp drive repaired before collapsing.
Meanwhile on the bridge, everyone is grimly resigned to dying, until at the last minute, the warp drive kicks in. They beat it out of there just ahead of the explosion, which disintegrates the Reliant and implodes the nebula. Amid the cries of relief, Kirk contacts the engine room to thank Scotty for performing another miracle. It is Dr. McCoy who responds, saying quietly, "Jim, you'd better get down here." Realizing that something is terribly wrong, Kirk automatically glances over to where Spock should be. Seeing his empty chair, a look of horror enters Kirk's eyes, and he races to the engine room.
Seeing Spock collapsed in the containment area, Kirk immediately throws himself at the door and has to be restrained from going in after his friend. He only stops struggling when McCoy tells him that he'll flood the room with radiation if he breaks in there now. Leaning against the glass, he desperately calls Spock's name. Incredibly Spock responds, getting up and unsteadily walking towards the sound of Kirk's voice; he obviously can no longer see, as he bumps into the glass. He slowly sinks to the floor, and Kirk does the same on the other side of the glass.
Spock tells Kirk not to grieve: it was the logical thing to do. We come full circle as Spock repeats his earlier words to Kirk, "The needs of the many outweigh..." As his voice falters, Kirk continues, "...the needs of the few," and Spock hoarsely completes, "or the one." He then says that he never took the Kobayachi Maru, and asks what Kirk thinks of his response. Weakening, Spock places his hand on the glass in the Vulcan hand salute. As Kirk places his hand opposite, Spock tells him to live long and prosper, and then dies. Kirk quietly says "No," and leans his head against the glass, overcome with loss.
Kirk gives the eulogy at Spock's funeral, remaining composed until the end of it when he chokes up while saying that "...of all the souls I have known in my travels, his was the most- human." Spock's coffin- a torpedo casing- is lowered into a torpedo tube as Scotty plays 'Amazing Grace" on the bagpipes, and it is then shot out into space.
Later in his quarters, Kirk is attempting to read the copy of A Tale of Two Cities which Spock gave him, but is struggling because his spectacles got broken during the battle with Khan. David comes to see him, and he says that Saavik was right- that Kirk had never really faced death. Kirk says no, not like this. Rather, he has always tricked death, cheated it, and then patted himself on the back for his ingenuity. David, who over the course of events has gained respect for Kirk and tries to comfort him. He then hesitatingly tells Kirk that he is proud to be his son. The two of them embrace.
On the bridge afterwards, everyone stares at what the Genesis wave has done to the nebula: formed a new planet out of its matter. As they gaze at it, Kirk quotes a few lines from the end of A Tale of Two Cities, and Carol asks him how he feels. He tells her that he feels young. The Enterprise heads to Ceti Alpha V to pick up the crew of the Reliant, and the last thing we see on the newly formed Genesis planet is Spock's coffin, resting on the surface.